diff --git a/gtsam/hybrid/HybridBayesNet.cpp b/gtsam/hybrid/HybridBayesNet.cpp index 7a46d7832..c598b7d62 100644 --- a/gtsam/hybrid/HybridBayesNet.cpp +++ b/gtsam/hybrid/HybridBayesNet.cpp @@ -36,7 +36,7 @@ DecisionTreeFactor::shared_ptr HybridBayesNet::discreteConditionals() const { for (auto &&conditional : *this) { if (conditional->isDiscrete()) { // Convert to a DecisionTreeFactor and add it to the main factor. - DecisionTreeFactor f(*conditional->asDiscreteConditional()); + DecisionTreeFactor f(*conditional->asDiscrete()); dtFactor = dtFactor * f; } } @@ -108,7 +108,7 @@ void HybridBayesNet::updateDiscreteConditionals( HybridConditional::shared_ptr conditional = this->at(i); if (conditional->isDiscrete()) { // std::cout << demangle(typeid(conditional).name()) << std::endl; - auto discrete = conditional->asDiscreteConditional(); + auto discrete = conditional->asDiscrete(); KeyVector frontals(discrete->frontals().begin(), discrete->frontals().end()); @@ -150,16 +150,11 @@ HybridBayesNet HybridBayesNet::prune(size_t maxNrLeaves) { // Go through all the conditionals in the // Bayes Net and prune them as per decisionTree. - for (size_t i = 0; i < this->size(); i++) { - HybridConditional::shared_ptr conditional = this->at(i); - - if (conditional->isHybrid()) { - GaussianMixture::shared_ptr gaussianMixture = conditional->asMixture(); - + for (auto &&conditional : *this) { + if (auto gm = conditional->asMixture()) { // Make a copy of the Gaussian mixture and prune it! - auto prunedGaussianMixture = - boost::make_shared(*gaussianMixture); - prunedGaussianMixture->prune(*decisionTree); + auto prunedGaussianMixture = boost::make_shared(*gm); + prunedGaussianMixture->prune(*decisionTree); // imperative :-( // Type-erase and add to the pruned Bayes Net fragment. prunedBayesNetFragment.push_back( @@ -186,7 +181,7 @@ GaussianConditional::shared_ptr HybridBayesNet::atGaussian(size_t i) const { /* ************************************************************************* */ DiscreteConditional::shared_ptr HybridBayesNet::atDiscrete(size_t i) const { - return at(i)->asDiscreteConditional(); + return at(i)->asDiscrete(); } /* ************************************************************************* */ @@ -194,16 +189,13 @@ GaussianBayesNet HybridBayesNet::choose( const DiscreteValues &assignment) const { GaussianBayesNet gbn; for (auto &&conditional : *this) { - if (conditional->isHybrid()) { + if (auto gm = conditional->asMixture()) { // If conditional is hybrid, select based on assignment. - GaussianMixture gm = *conditional->asMixture(); - gbn.push_back(gm(assignment)); - - } else if (conditional->isContinuous()) { + gbn.push_back((*gm)(assignment)); + } else if (auto gc = conditional->asGaussian()) { // If continuous only, add Gaussian conditional. - gbn.push_back((conditional->asGaussian())); - - } else if (conditional->isDiscrete()) { + gbn.push_back(gc); + } else if (auto dc = conditional->asDiscrete()) { // If conditional is discrete-only, we simply continue. continue; } @@ -218,23 +210,47 @@ HybridValues HybridBayesNet::optimize() const { DiscreteBayesNet discrete_bn; for (auto &&conditional : *this) { if (conditional->isDiscrete()) { - discrete_bn.push_back(conditional->asDiscreteConditional()); + discrete_bn.push_back(conditional->asDiscrete()); } } DiscreteValues mpe = DiscreteFactorGraph(discrete_bn).optimize(); // Given the MPE, compute the optimal continuous values. - GaussianBayesNet gbn = this->choose(mpe); + GaussianBayesNet gbn = choose(mpe); return HybridValues(mpe, gbn.optimize()); } /* ************************************************************************* */ VectorValues HybridBayesNet::optimize(const DiscreteValues &assignment) const { - GaussianBayesNet gbn = this->choose(assignment); + GaussianBayesNet gbn = choose(assignment); return gbn.optimize(); } +/* ************************************************************************* */ +double HybridBayesNet::evaluate(const HybridValues &values) const { + const DiscreteValues &discreteValues = values.discrete(); + const VectorValues &continuousValues = values.continuous(); + + double logDensity = 0.0, probability = 1.0; + + // Iterate over each conditional. + for (auto &&conditional : *this) { + if (auto gm = conditional->asMixture()) { + const auto component = (*gm)(discreteValues); + logDensity += component->logDensity(continuousValues); + } else if (auto gc = conditional->asGaussian()) { + // If continuous only, evaluate the probability and multiply. + logDensity += gc->logDensity(continuousValues); + } else if (auto dc = conditional->asDiscrete()) { + // Conditional is discrete-only, so return its probability. + probability *= dc->operator()(discreteValues); + } + } + + return probability * exp(logDensity); +} + /* ************************************************************************* */ HybridValues HybridBayesNet::sample(const HybridValues &given, std::mt19937_64 *rng) const { @@ -242,7 +258,7 @@ HybridValues HybridBayesNet::sample(const HybridValues &given, for (auto &&conditional : *this) { if (conditional->isDiscrete()) { // If conditional is discrete-only, we add to the discrete Bayes net. - dbn.push_back(conditional->asDiscreteConditional()); + dbn.push_back(conditional->asDiscrete()); } } // Sample a discrete assignment. @@ -273,7 +289,7 @@ HybridValues HybridBayesNet::sample() const { /* ************************************************************************* */ double HybridBayesNet::error(const VectorValues &continuousValues, const DiscreteValues &discreteValues) const { - GaussianBayesNet gbn = this->choose(discreteValues); + GaussianBayesNet gbn = choose(discreteValues); return gbn.error(continuousValues); } @@ -284,23 +300,20 @@ AlgebraicDecisionTree HybridBayesNet::error( // Iterate over each conditional. for (auto &&conditional : *this) { - if (conditional->isHybrid()) { + if (auto gm = conditional->asMixture()) { // If conditional is hybrid, select based on assignment and compute error. - GaussianMixture::shared_ptr gm = conditional->asMixture(); AlgebraicDecisionTree conditional_error = gm->error(continuousValues); error_tree = error_tree + conditional_error; - - } else if (conditional->isContinuous()) { + } else if (auto gc = conditional->asGaussian()) { // If continuous only, get the (double) error // and add it to the error_tree - double error = conditional->asGaussian()->error(continuousValues); + double error = gc->error(continuousValues); // Add the computed error to every leaf of the error tree. error_tree = error_tree.apply( [error](double leaf_value) { return leaf_value + error; }); - - } else if (conditional->isDiscrete()) { + } else if (auto dc = conditional->asDiscrete()) { // Conditional is discrete-only, we skip. continue; } diff --git a/gtsam/hybrid/HybridBayesNet.h b/gtsam/hybrid/HybridBayesNet.h index 1e6bebf1a..4e41cb11d 100644 --- a/gtsam/hybrid/HybridBayesNet.h +++ b/gtsam/hybrid/HybridBayesNet.h @@ -95,6 +95,14 @@ class GTSAM_EXPORT HybridBayesNet : public BayesNet { */ GaussianBayesNet choose(const DiscreteValues &assignment) const; + /// Evaluate hybrid probability density for given HybridValues. + double evaluate(const HybridValues &values) const; + + /// Evaluate hybrid probability density for given HybridValues, sugar. + double operator()(const HybridValues &values) const { + return evaluate(values); + } + /** * @brief Solve the HybridBayesNet by first computing the MPE of all the * discrete variables and then optimizing the continuous variables based on diff --git a/gtsam/hybrid/HybridBayesTree.cpp b/gtsam/hybrid/HybridBayesTree.cpp index 8fdedab44..ed70a0aa9 100644 --- a/gtsam/hybrid/HybridBayesTree.cpp +++ b/gtsam/hybrid/HybridBayesTree.cpp @@ -49,7 +49,7 @@ HybridValues HybridBayesTree::optimize() const { // The root should be discrete only, we compute the MPE if (root_conditional->isDiscrete()) { - dbn.push_back(root_conditional->asDiscreteConditional()); + dbn.push_back(root_conditional->asDiscrete()); mpe = DiscreteFactorGraph(dbn).optimize(); } else { throw std::runtime_error( @@ -147,7 +147,7 @@ VectorValues HybridBayesTree::optimize(const DiscreteValues& assignment) const { /* ************************************************************************* */ void HybridBayesTree::prune(const size_t maxNrLeaves) { auto decisionTree = - this->roots_.at(0)->conditional()->asDiscreteConditional(); + this->roots_.at(0)->conditional()->asDiscrete(); DecisionTreeFactor prunedDecisionTree = decisionTree->prune(maxNrLeaves); decisionTree->root_ = prunedDecisionTree.root_; diff --git a/gtsam/hybrid/HybridConditional.h b/gtsam/hybrid/HybridConditional.h index 050f10290..db03ba59c 100644 --- a/gtsam/hybrid/HybridConditional.h +++ b/gtsam/hybrid/HybridConditional.h @@ -131,34 +131,29 @@ class GTSAM_EXPORT HybridConditional /** * @brief Return HybridConditional as a GaussianMixture - * - * @return GaussianMixture::shared_ptr + * @return nullptr if not a mixture + * @return GaussianMixture::shared_ptr otherwise */ GaussianMixture::shared_ptr asMixture() { - if (!isHybrid()) throw std::invalid_argument("Not a mixture"); - return boost::static_pointer_cast(inner_); + return boost::dynamic_pointer_cast(inner_); } /** * @brief Return HybridConditional as a GaussianConditional - * - * @return GaussianConditional::shared_ptr + * @return nullptr if not a GaussianConditional + * @return GaussianConditional::shared_ptr otherwise */ GaussianConditional::shared_ptr asGaussian() { - if (!isContinuous()) - throw std::invalid_argument("Not a continuous conditional"); - return boost::static_pointer_cast(inner_); + return boost::dynamic_pointer_cast(inner_); } /** * @brief Return conditional as a DiscreteConditional - * + * @return nullptr if not a DiscreteConditional * @return DiscreteConditional::shared_ptr */ - DiscreteConditional::shared_ptr asDiscreteConditional() { - if (!isDiscrete()) - throw std::invalid_argument("Not a discrete conditional"); - return boost::static_pointer_cast(inner_); + DiscreteConditional::shared_ptr asDiscrete() { + return boost::dynamic_pointer_cast(inner_); } /// @} diff --git a/gtsam/hybrid/HybridValues.h b/gtsam/hybrid/HybridValues.h index 4928f9384..944fe17e6 100644 --- a/gtsam/hybrid/HybridValues.h +++ b/gtsam/hybrid/HybridValues.h @@ -78,10 +78,10 @@ class GTSAM_EXPORT HybridValues { /// @{ /// Return the discrete MPE assignment - DiscreteValues discrete() const { return discrete_; } + const DiscreteValues& discrete() const { return discrete_; } /// Return the delta update for the continuous vectors - VectorValues continuous() const { return continuous_; } + const VectorValues& continuous() const { return continuous_; } /// Check whether a variable with key \c j exists in DiscreteValue. bool existsDiscrete(Key j) { return (discrete_.find(j) != discrete_.end()); }; diff --git a/gtsam/hybrid/tests/testHybridBayesNet.cpp b/gtsam/hybrid/tests/testHybridBayesNet.cpp index 3e3fab376..d22087f47 100644 --- a/gtsam/hybrid/tests/testHybridBayesNet.cpp +++ b/gtsam/hybrid/tests/testHybridBayesNet.cpp @@ -36,36 +36,80 @@ using noiseModel::Isotropic; using symbol_shorthand::M; using symbol_shorthand::X; -static const DiscreteKey Asia(0, 2); +static const Key asiaKey = 0; +static const DiscreteKey Asia(asiaKey, 2); /* ****************************************************************************/ -// Test creation +// Test creation of a pure discrete Bayes net. TEST(HybridBayesNet, Creation) { HybridBayesNet bayesNet; - bayesNet.add(Asia, "99/1"); DiscreteConditional expected(Asia, "99/1"); - CHECK(bayesNet.atDiscrete(0)); - auto& df = *bayesNet.atDiscrete(0); - EXPECT(df.equals(expected)); + EXPECT(assert_equal(expected, *bayesNet.atDiscrete(0))); } /* ****************************************************************************/ -// Test adding a bayes net to another one. +// Test adding a Bayes net to another one. TEST(HybridBayesNet, Add) { HybridBayesNet bayesNet; - bayesNet.add(Asia, "99/1"); - DiscreteConditional expected(Asia, "99/1"); - HybridBayesNet other; other.push_back(bayesNet); EXPECT(bayesNet.equals(other)); } +/* ****************************************************************************/ +// Test evaluate for a pure discrete Bayes net P(Asia). +TEST(HybridBayesNet, evaluatePureDiscrete) { + HybridBayesNet bayesNet; + bayesNet.add(Asia, "99/1"); + HybridValues values; + values.insert(asiaKey, 0); + EXPECT_DOUBLES_EQUAL(0.99, bayesNet.evaluate(values), 1e-9); +} + +/* ****************************************************************************/ +// Test evaluate for a hybrid Bayes net P(X0|X1) P(X1|Asia) P(Asia). +TEST(HybridBayesNet, evaluateHybrid) { + const auto continuousConditional = GaussianConditional::FromMeanAndStddev( + X(0), 2 * I_1x1, X(1), Vector1(-4.0), 5.0); + + const SharedDiagonal model0 = noiseModel::Diagonal::Sigmas(Vector1(2.0)), + model1 = noiseModel::Diagonal::Sigmas(Vector1(3.0)); + + const auto conditional0 = boost::make_shared( + X(1), Vector1::Constant(5), I_1x1, model0), + conditional1 = boost::make_shared( + X(1), Vector1::Constant(2), I_1x1, model1); + + // TODO(dellaert): creating and adding mixture is clumsy. + const auto mixture = GaussianMixture::FromConditionals( + {X(1)}, {}, {Asia}, {conditional0, conditional1}); + + // Create hybrid Bayes net. + HybridBayesNet bayesNet; + bayesNet.push_back(HybridConditional( + boost::make_shared(continuousConditional))); + bayesNet.push_back( + HybridConditional(boost::make_shared(mixture))); + bayesNet.add(Asia, "99/1"); + + // Create values at which to evaluate. + HybridValues values; + values.insert(asiaKey, 0); + values.insert(X(0), Vector1(-6)); + values.insert(X(1), Vector1(1)); + + const double conditionalProbability = + continuousConditional.evaluate(values.continuous()); + const double mixtureProbability = conditional0->evaluate(values.continuous()); + EXPECT_DOUBLES_EQUAL(conditionalProbability * mixtureProbability * 0.99, + bayesNet.evaluate(values), 1e-9); +} + /* ****************************************************************************/ // Test choosing an assignment of conditionals TEST(HybridBayesNet, Choose) { @@ -105,7 +149,7 @@ TEST(HybridBayesNet, Choose) { } /* ****************************************************************************/ -// Test bayes net optimize +// Test Bayes net optimize TEST(HybridBayesNet, OptimizeAssignment) { Switching s(4); @@ -139,7 +183,7 @@ TEST(HybridBayesNet, OptimizeAssignment) { } /* ****************************************************************************/ -// Test bayes net optimize +// Test Bayes net optimize TEST(HybridBayesNet, Optimize) { Switching s(4); @@ -203,7 +247,7 @@ TEST(HybridBayesNet, Error) { // regression EXPECT(assert_equal(expected_error, error_tree, 1e-9)); - // Error on pruned bayes net + // Error on pruned Bayes net auto prunedBayesNet = hybridBayesNet->prune(2); auto pruned_error_tree = prunedBayesNet.error(delta.continuous()); @@ -238,7 +282,7 @@ TEST(HybridBayesNet, Error) { } /* ****************************************************************************/ -// Test bayes net pruning +// Test Bayes net pruning TEST(HybridBayesNet, Prune) { Switching s(4); @@ -256,7 +300,7 @@ TEST(HybridBayesNet, Prune) { } /* ****************************************************************************/ -// Test bayes net updateDiscreteConditionals +// Test Bayes net updateDiscreteConditionals TEST(HybridBayesNet, UpdateDiscreteConditionals) { Switching s(4); @@ -273,8 +317,7 @@ TEST(HybridBayesNet, UpdateDiscreteConditionals) { EXPECT_LONGS_EQUAL(maxNrLeaves + 2 /*2 zero leaves*/, prunedDecisionTree->nrLeaves()); - auto original_discrete_conditionals = - *(hybridBayesNet->at(4)->asDiscreteConditional()); + auto original_discrete_conditionals = *(hybridBayesNet->at(4)->asDiscrete()); // Prune! hybridBayesNet->prune(maxNrLeaves); @@ -294,8 +337,7 @@ TEST(HybridBayesNet, UpdateDiscreteConditionals) { }; // Get the pruned discrete conditionals as an AlgebraicDecisionTree - auto pruned_discrete_conditionals = - hybridBayesNet->at(4)->asDiscreteConditional(); + auto pruned_discrete_conditionals = hybridBayesNet->at(4)->asDiscrete(); auto discrete_conditional_tree = boost::dynamic_pointer_cast( pruned_discrete_conditionals); @@ -358,7 +400,7 @@ TEST(HybridBayesNet, Sampling) { // Sample HybridValues sample = bn->sample(&gen); - discrete_samples.push_back(sample.discrete()[M(0)]); + discrete_samples.push_back(sample.discrete().at(M(0))); if (i == 0) { average_continuous.insert(sample.continuous()); diff --git a/gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp b/gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp index 7877461b6..55e4c28ad 100644 --- a/gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp +++ b/gtsam/hybrid/tests/testHybridGaussianFactorGraph.cpp @@ -133,7 +133,7 @@ TEST(HybridGaussianFactorGraph, eliminateFullSequentialEqualChance) { auto result = hfg.eliminateSequential(Ordering::ColamdConstrainedLast(hfg, {M(1)})); - auto dc = result->at(2)->asDiscreteConditional(); + auto dc = result->at(2)->asDiscrete(); DiscreteValues dv; dv[M(1)] = 0; EXPECT_DOUBLES_EQUAL(1, dc->operator()(dv), 1e-3); diff --git a/gtsam/hybrid/tests/testHybridGaussianISAM.cpp b/gtsam/hybrid/tests/testHybridGaussianISAM.cpp index 18ce7f10e..11bd3b415 100644 --- a/gtsam/hybrid/tests/testHybridGaussianISAM.cpp +++ b/gtsam/hybrid/tests/testHybridGaussianISAM.cpp @@ -111,8 +111,7 @@ TEST(HybridGaussianElimination, IncrementalInference) { // Run update step isam.update(graph1); - auto discreteConditional_m0 = - isam[M(0)]->conditional()->asDiscreteConditional(); + auto discreteConditional_m0 = isam[M(0)]->conditional()->asDiscrete(); EXPECT(discreteConditional_m0->keys() == KeyVector({M(0)})); /********************************************************/ @@ -170,10 +169,10 @@ TEST(HybridGaussianElimination, IncrementalInference) { DiscreteValues m00; m00[M(0)] = 0, m00[M(1)] = 0; DiscreteConditional decisionTree = - *(*discreteBayesTree)[M(1)]->conditional()->asDiscreteConditional(); + *(*discreteBayesTree)[M(1)]->conditional()->asDiscrete(); double m00_prob = decisionTree(m00); - auto discreteConditional = isam[M(1)]->conditional()->asDiscreteConditional(); + auto discreteConditional = isam[M(1)]->conditional()->asDiscrete(); // Test if the probability values are as expected with regression tests. DiscreteValues assignment; @@ -535,7 +534,7 @@ TEST(HybridGaussianISAM, NonTrivial) { // The final discrete graph should not be empty since we have eliminated // all continuous variables. - auto discreteTree = inc[M(3)]->conditional()->asDiscreteConditional(); + auto discreteTree = inc[M(3)]->conditional()->asDiscrete(); EXPECT_LONGS_EQUAL(3, discreteTree->size()); // Test if the optimal discrete mode assignment is (1, 1, 1). diff --git a/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp b/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp index 3bdb5ed1e..8801a8946 100644 --- a/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp +++ b/gtsam/hybrid/tests/testHybridNonlinearISAM.cpp @@ -124,8 +124,7 @@ TEST(HybridNonlinearISAM, IncrementalInference) { isam.update(graph1, initial); HybridGaussianISAM bayesTree = isam.bayesTree(); - auto discreteConditional_m0 = - bayesTree[M(0)]->conditional()->asDiscreteConditional(); + auto discreteConditional_m0 = bayesTree[M(0)]->conditional()->asDiscrete(); EXPECT(discreteConditional_m0->keys() == KeyVector({M(0)})); /********************************************************/ @@ -187,11 +186,11 @@ TEST(HybridNonlinearISAM, IncrementalInference) { DiscreteValues m00; m00[M(0)] = 0, m00[M(1)] = 0; DiscreteConditional decisionTree = - *(*discreteBayesTree)[M(1)]->conditional()->asDiscreteConditional(); + *(*discreteBayesTree)[M(1)]->conditional()->asDiscrete(); double m00_prob = decisionTree(m00); auto discreteConditional = - bayesTree[M(1)]->conditional()->asDiscreteConditional(); + bayesTree[M(1)]->conditional()->asDiscrete(); // Test if the probability values are as expected with regression tests. DiscreteValues assignment; @@ -558,7 +557,7 @@ TEST(HybridNonlinearISAM, NonTrivial) { // The final discrete graph should not be empty since we have eliminated // all continuous variables. - auto discreteTree = bayesTree[M(3)]->conditional()->asDiscreteConditional(); + auto discreteTree = bayesTree[M(3)]->conditional()->asDiscrete(); EXPECT_LONGS_EQUAL(3, discreteTree->size()); // Test if the optimal discrete mode assignment is (1, 1, 1). diff --git a/gtsam/linear/GaussianBayesNet.cpp b/gtsam/linear/GaussianBayesNet.cpp index 229d4a932..4c1338435 100644 --- a/gtsam/linear/GaussianBayesNet.cpp +++ b/gtsam/linear/GaussianBayesNet.cpp @@ -224,5 +224,19 @@ namespace gtsam { } /* ************************************************************************* */ + double GaussianBayesNet::logDensity(const VectorValues& x) const { + double sum = 0.0; + for (const auto& conditional : *this) { + if (conditional) sum += conditional->logDensity(x); + } + return sum; + } + + /* ************************************************************************* */ + double GaussianBayesNet::evaluate(const VectorValues& x) const { + return exp(logDensity(x)); + } + + /* ************************************************************************* */ } // namespace gtsam diff --git a/gtsam/linear/GaussianBayesNet.h b/gtsam/linear/GaussianBayesNet.h index e81d6af33..426d3bd83 100644 --- a/gtsam/linear/GaussianBayesNet.h +++ b/gtsam/linear/GaussianBayesNet.h @@ -88,6 +88,26 @@ namespace gtsam { /// @name Standard Interface /// @{ + /** + * Calculate probability density for given values `x`: + * exp(-error(x)) / sqrt((2*pi)^n*det(Sigma)) + * where x is the vector of values, and Sigma is the covariance matrix. + * Note that error(x)=0.5*e'*e includes the 0.5 factor already. + */ + double evaluate(const VectorValues& x) const; + + /// Evaluate probability density, sugar. + double operator()(const VectorValues& x) const { + return evaluate(x); + } + + /** + * Calculate log-density for given values `x`: + * -error(x) - 0.5 * n*log(2*pi) - 0.5 * log det(Sigma) + * where x is the vector of values, and Sigma is the covariance matrix. + */ + double logDensity(const VectorValues& x) const; + /// Solve the GaussianBayesNet, i.e. return \f$ x = R^{-1}*d \f$, by /// back-substitution VectorValues optimize() const; diff --git a/gtsam/linear/GaussianConditional.cpp b/gtsam/linear/GaussianConditional.cpp index 4597156bc..5e8a193cf 100644 --- a/gtsam/linear/GaussianConditional.cpp +++ b/gtsam/linear/GaussianConditional.cpp @@ -169,6 +169,21 @@ double GaussianConditional::logDeterminant() const { return logDet; } +/* ************************************************************************* */ +// density = exp(-error(x)) / sqrt((2*pi)^n*det(Sigma)) +// log = -error(x) - 0.5 * n*log(2*pi) - 0.5 * log det(Sigma) +double GaussianConditional::logDensity(const VectorValues& x) const { + constexpr double log2pi = 1.8378770664093454835606594728112; + size_t n = d().size(); + // log det(Sigma)) = - 2.0 * logDeterminant() + return - error(x) - 0.5 * n * log2pi + logDeterminant(); +} + +/* ************************************************************************* */ +double GaussianConditional::evaluate(const VectorValues& x) const { + return exp(logDensity(x)); +} + /* ************************************************************************* */ VectorValues GaussianConditional::solve(const VectorValues& x) const { // Concatenate all vector values that correspond to parent variables diff --git a/gtsam/linear/GaussianConditional.h b/gtsam/linear/GaussianConditional.h index 8af7f6602..a72a73973 100644 --- a/gtsam/linear/GaussianConditional.h +++ b/gtsam/linear/GaussianConditional.h @@ -121,6 +121,26 @@ namespace gtsam { /// @name Standard Interface /// @{ + /** + * Calculate probability density for given values `x`: + * exp(-error(x)) / sqrt((2*pi)^n*det(Sigma)) + * where x is the vector of values, and Sigma is the covariance matrix. + * Note that error(x)=0.5*e'*e includes the 0.5 factor already. + */ + double evaluate(const VectorValues& x) const; + + /// Evaluate probability density, sugar. + double operator()(const VectorValues& x) const { + return evaluate(x); + } + + /** + * Calculate log-density for given values `x`: + * -error(x) - 0.5 * n*log(2*pi) - 0.5 * log det(Sigma) + * where x is the vector of values, and Sigma is the covariance matrix. + */ + double logDensity(const VectorValues& x) const; + /** Return a view of the upper-triangular R block of the conditional */ constABlock R() const { return Ab_.range(0, nrFrontals()); } @@ -134,27 +154,31 @@ namespace gtsam { const constBVector d() const { return BaseFactor::getb(); } /** - * @brief Compute the log determinant of the Gaussian conditional. - * The determinant is computed using the R matrix, which is upper - * triangular. - * For numerical stability, the determinant is computed in log - * form, so it is a summation rather than a multiplication. + * @brief Compute the determinant of the R matrix. * - * @return double - */ - double logDeterminant() const; - - /** - * @brief Compute the determinant of the conditional from the - * upper-triangular R matrix. - * - * The determinant is computed in log form (hence summation) for numerical - * stability and then exponentiated. + * The determinant is computed in log form using logDeterminant for + * numerical stability and then exponentiated. + * + * Note, the covariance matrix \f$ \Sigma = (R^T R)^{-1} \f$, and hence + * \f$ \det(\Sigma) = 1 / \det(R^T R) = 1 / determinant()^ 2 \f$. * * @return double */ double determinant() const { return exp(this->logDeterminant()); } + /** + * @brief Compute the log determinant of the R matrix. + * + * For numerical stability, the determinant is computed in log + * form, so it is a summation rather than a multiplication. + * + * Note, the covariance matrix \f$ \Sigma = (R^T R)^{-1} \f$, and hence + * \f$ \log \det(\Sigma) = - \log \det(R^T R) = - 2 logDeterminant() \f$. + * + * @return double + */ + double logDeterminant() const; + /** * Solves a conditional Gaussian and writes the solution into the entries of * \c x for each frontal variable of the conditional. The parents are diff --git a/gtsam/linear/tests/testGaussianBayesNet.cpp b/gtsam/linear/tests/testGaussianBayesNet.cpp index 2b125265f..771a24631 100644 --- a/gtsam/linear/tests/testGaussianBayesNet.cpp +++ b/gtsam/linear/tests/testGaussianBayesNet.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------------- - * GTSAM Copyright 2010, Georgia Tech Research Corporation, + * GTSAM Copyright 2010-2022, Georgia Tech Research Corporation, * Atlanta, Georgia 30332-0415 * All Rights Reserved * Authors: Frank Dellaert, et al. (see THANKS for the full author list) @@ -67,6 +67,36 @@ TEST( GaussianBayesNet, Matrix ) EXPECT(assert_equal(d,d1)); } +/* ************************************************************************* */ +// Check that the evaluate function matches direct calculation with R. +TEST(GaussianBayesNet, Evaluate1) { + // Let's evaluate at the mean + const VectorValues mean = smallBayesNet.optimize(); + + // We get the matrix, which has noise model applied! + const Matrix R = smallBayesNet.matrix().first; + const Matrix invSigma = R.transpose() * R; + + // The Bayes net is a Gaussian density ~ exp (-0.5*(Rx-d)'*(Rx-d)) + // which at the mean is 1.0! So, the only thing we need to calculate is + // the normalization constant 1.0/sqrt((2*pi*Sigma).det()). + // The covariance matrix inv(Sigma) = R'*R, so the determinant is + const double expected = sqrt((invSigma / (2 * M_PI)).determinant()); + const double actual = smallBayesNet.evaluate(mean); + EXPECT_DOUBLES_EQUAL(expected, actual, 1e-9); +} + +// Check the evaluate with non-unit noise. +TEST(GaussianBayesNet, Evaluate2) { + // See comments in test above. + const VectorValues mean = noisyBayesNet.optimize(); + const Matrix R = noisyBayesNet.matrix().first; + const Matrix invSigma = R.transpose() * R; + const double expected = sqrt((invSigma / (2 * M_PI)).determinant()); + const double actual = noisyBayesNet.evaluate(mean); + EXPECT_DOUBLES_EQUAL(expected, actual, 1e-9); +} + /* ************************************************************************* */ TEST( GaussianBayesNet, NoisyMatrix ) { @@ -142,14 +172,18 @@ TEST( GaussianBayesNet, optimize3 ) } /* ************************************************************************* */ -TEST(GaussianBayesNet, sample) { - GaussianBayesNet gbn; - Matrix A1 = (Matrix(2, 2) << 1., 2., 3., 4.).finished(); - const Vector2 mean(20, 40), b(10, 10); - const double sigma = 0.01; +namespace sampling { +static Matrix A1 = (Matrix(2, 2) << 1., 2., 3., 4.).finished(); +static const Vector2 mean(20, 40), b(10, 10); +static const double sigma = 0.01; +static const GaussianBayesNet gbn = + list_of(GaussianConditional::FromMeanAndStddev(X(0), A1, X(1), b, sigma))( + GaussianDensity::FromMeanAndStddev(X(1), mean, sigma)); +} // namespace sampling - gbn.add(GaussianConditional::FromMeanAndStddev(X(0), A1, X(1), b, sigma)); - gbn.add(GaussianDensity::FromMeanAndStddev(X(1), mean, sigma)); +/* ************************************************************************* */ +TEST(GaussianBayesNet, sample) { + using namespace sampling; auto actual = gbn.sample(); EXPECT_LONGS_EQUAL(2, actual.size()); @@ -165,6 +199,23 @@ TEST(GaussianBayesNet, sample) { // EXPECT(assert_equal(Vector2(110.032083, 230.039811), actual[X(0)], 1e-5)); } +/* ************************************************************************* */ +// Do Monte Carlo integration of square deviation, should be equal to 9.0. +TEST(GaussianBayesNet, MonteCarloIntegration) { + GaussianBayesNet gbn; + gbn.push_back(noisyBayesNet.at(1)); + + double sum = 0.0; + constexpr size_t N = 1000; + // loop for N samples: + for (size_t i = 0; i < N; i++) { + const auto X_i = gbn.sample(); + sum += pow(X_i[_y_].x() - 5.0, 2.0); + } + // Expected is variance = 3*3 + EXPECT_DOUBLES_EQUAL(9.0, sum / N, 0.5); // Pretty high. +} + /* ************************************************************************* */ TEST(GaussianBayesNet, ordering) { diff --git a/gtsam/linear/tests/testGaussianConditional.cpp b/gtsam/linear/tests/testGaussianConditional.cpp index 6ec06a0ce..20d730856 100644 --- a/gtsam/linear/tests/testGaussianConditional.cpp +++ b/gtsam/linear/tests/testGaussianConditional.cpp @@ -130,6 +130,75 @@ TEST( GaussianConditional, equals ) EXPECT( expected.equals(actual) ); } +/* ************************************************************************* */ +namespace density { +static const Key key = 77; +static constexpr double sigma = 3.0; +static const auto unitPrior = + GaussianConditional(key, Vector1::Constant(5), I_1x1), + widerPrior = GaussianConditional( + key, Vector1::Constant(5), I_1x1, + noiseModel::Isotropic::Sigma(1, sigma)); +} // namespace density + +/* ************************************************************************* */ +// Check that the evaluate function matches direct calculation with R. +TEST(GaussianConditional, Evaluate1) { + // Let's evaluate at the mean + const VectorValues mean = density::unitPrior.solve(VectorValues()); + + // We get the Hessian matrix, which has noise model applied! + const Matrix invSigma = density::unitPrior.information(); + + // A Gaussian density ~ exp (-0.5*(Rx-d)'*(Rx-d)) + // which at the mean is 1.0! So, the only thing we need to calculate is + // the normalization constant 1.0/sqrt((2*pi*Sigma).det()). + // The covariance matrix inv(Sigma) = R'*R, so the determinant is + const double expected = sqrt((invSigma / (2 * M_PI)).determinant()); + const double actual = density::unitPrior.evaluate(mean); + EXPECT_DOUBLES_EQUAL(expected, actual, 1e-9); + + using density::key; + using density::sigma; + + // Let's numerically integrate and see that we integrate to 1.0. + double integral = 0.0; + // Loop from -5*sigma to 5*sigma in 0.1*sigma steps: + for (double x = -5.0 * sigma; x <= 5.0 * sigma; x += 0.1 * sigma) { + VectorValues xValues; + xValues.insert(key, mean.at(key) + Vector1(x)); + const double density = density::unitPrior.evaluate(xValues); + integral += 0.1 * sigma * density; + } + EXPECT_DOUBLES_EQUAL(1.0, integral, 1e-9); +} + +/* ************************************************************************* */ +// Check the evaluate with non-unit noise. +TEST(GaussianConditional, Evaluate2) { + // See comments in test above. + const VectorValues mean = density::widerPrior.solve(VectorValues()); + const Matrix R = density::widerPrior.R(); + const Matrix invSigma = density::widerPrior.information(); + const double expected = sqrt((invSigma / (2 * M_PI)).determinant()); + const double actual = density::widerPrior.evaluate(mean); + EXPECT_DOUBLES_EQUAL(expected, actual, 1e-9); + + using density::key; + using density::sigma; + + // Let's numerically integrate and see that we integrate to 1.0. + double integral = 0.0; + // Loop from -5*sigma to 5*sigma in 0.1*sigma steps: + for (double x = -5.0 * sigma; x <= 5.0 * sigma; x += 0.1 * sigma) { + VectorValues xValues; + xValues.insert(key, mean.at(key) + Vector1(x)); + const double density = density::widerPrior.evaluate(xValues); + integral += 0.1 * sigma * density; + } + EXPECT_DOUBLES_EQUAL(1.0, integral, 1e-5); +} + /* ************************************************************************* */ TEST( GaussianConditional, solve ) {